RE: Question Re Calling nmfe7 from R
Dear all, thank you all for your valuable input! I'm gladly reporting
back that the problem was resolved.
I'd like to give more background information since I wasn't clear on what
I was doing and what type of error message I received. Here's more
details.
Background:
I need to call NONMEM from R because of the need to automate procedures
involving NONMEM runs and sequential data formatting, such as bootstrap
for sequential PK/PD analysis. NOMMEM is called in R by the following
command: system('nmfe7.bat control3 control3.res')
After my NONMEM7.1.2 upgrade, I got 'ifort does not exist' type of error
message, when I opened a command window by 'run cmd' from the start menu,
or from Command Prompt, or call NONMEM from R like I did before. But
if I opened a command window by
Start menu > All Programs > Intel(R) Software Development Tools > Intel(R)
Visula Fortran Compiler Professional 11.1.048 > Fortran Buid Environment
for applications running on IA-32 , NONMEM runs OK.
Resolution:
Following Bill's suggestion, I located the NONMEM-PDx-Pop-support.pdf file
from the NM712Upgrade directory, and fixed the system environment
variables. Now I'm able to run NONMEM in both DOS command window and R.
Best regards,
Shelley
========================================
Xiao Hu (Shelley), Ph.D.
Senior Scientist,
Clinical Pharmacology and Pharmacometrics
Biogen Idec, Inc.
14 Cambridge Center
Cambridge, MA 02142
"Bachman, William" <[email protected]>
Sent by: [email protected]
04-May-2011 01:14 PM
Message Size: 15.4 KB
To
"Bill Knebel" <[email protected]>, "Xiao Hu" <[email protected]>
cc
<[email protected]>
Subject
RE: [NMusers] Question Re Calling nmfe7 from R
I think the real underlying issue is that the system environment variables
have not been set for Intel Fortran and Microsoft Visual Studio. The
Intel build environment window is being used to run NONMEM so R cannot
call NONMEM (whether it is just a run or any function of MIfuns). The
NONMEM release CD contains a document that describes how to set
environment variables for Intel Fortran and Microsoft Visual Studio
(NONMEM-PDx-Pop-Support.pdf). Then R or R/MIfuns will be able to call
NONMEM.
William J. Bachman, Ph.D.
Director, Pharmacometrics R&D
Icon Development Solutions
6031 University Blvd., Suite 300
Ellicott City, MD 21043
Office 215-616-8699
[email protected]
Quoted reply history
From: [email protected] [mailto:[email protected]]
On Behalf Of Bill Knebel
Sent: Wednesday, May 04, 2011 12:37 PM
To: Xiao Hu
Cc: [email protected]
Subject: Re: [NMusers] Question Re Calling nmfe7 from R
Shelley,
You may want to consider the R package (MIfuns), developed and released by
Metrum Institute. It is available on CRAN (R package repository) and via
googlecode ( http://code.google.com/p/mifuns/). Using this package along
with the free NONMEM installer (NMQual), also available via googlecode (
http://code.google.com/p/nmqual/) , will allow you to call nonmem from R
and also provides a complete set of R functions for performing analyses,
preparing data sets, generating and analyzing bootstraps, and generating
post analyses tables and figures. It is more than just running NONMEM from
R so you will likely find it helpful in the other aspects of data prep and
modeling I just mentioned.
Regards,
Bill
On May 4, 2011, at 11:50 AM, Xiao Hu wrote:
Dear NONMEM users,
I recently have NONMEM 7.1.0 upgraded to 7.1.2, which only worked in Intel
Fortran compiler, but not in DOS.
When I tried to call nmfe7 from R, it apparently called DOS command and
failed to run. Is there a way to link nmfe7 to Intel, instead of DOS?
I've been waiting for an answer for my IT rep for two weeks and am
wondering if I can get some guidance from our discussion group.
Best regards,
Shelley
========================================
Xiao Hu (Shelley), Ph.D.
Senior Scientist,
Clinical Pharmacology and Pharmacometrics
Biogen Idec, Inc.
14 Cambridge Center
Cambridge, MA 02142